[2024-01-24 15:19:03,337] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:19:03,339] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:19:03,339] [INFO] DQC Reference Directory: /var/lib/cwl/stgf78ed2a0-4065-43c2-8680-4ec6b4336702/dqc_reference
[2024-01-24 15:19:04,580] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:19:04,581] [INFO] Task started: Prodigal
[2024-01-24 15:19:04,581] [INFO] Running command: gunzip -c /var/lib/cwl/stg27b291b5-b015-4fb8-b074-85eca2a4ccff/GCF_003596335.1_ASM359633v1_genomic.fna.gz | prodigal -d GCF_003596335.1_ASM359633v1_genomic.fna/cds.fna -a GCF_003596335.1_ASM359633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:15,351] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:15,352] [INFO] Task started: HMMsearch
[2024-01-24 15:19:15,352] [INFO] Running command: hmmsearch --tblout GCF_003596335.1_ASM359633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf78ed2a0-4065-43c2-8680-4ec6b4336702/dqc_reference/reference_markers.hmm GCF_003596335.1_ASM359633v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:15,659] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:15,661] [INFO] Found 6/6 markers.
[2024-01-24 15:19:15,703] [INFO] Query marker FASTA was written to GCF_003596335.1_ASM359633v1_genomic.fna/markers.fasta
[2024-01-24 15:19:15,704] [INFO] Task started: Blastn
[2024-01-24 15:19:15,704] [INFO] Running command: blastn -query GCF_003596335.1_ASM359633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf78ed2a0-4065-43c2-8680-4ec6b4336702/dqc_reference/reference_markers.fasta -out GCF_003596335.1_ASM359633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:16,471] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:16,475] [INFO] Selected 26 target genomes.
[2024-01-24 15:19:16,476] [INFO] Target genome list was writen to GCF_003596335.1_ASM359633v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:16,786] [INFO] Task started: fastANI
[2024-01-24 15:19:16,786] [INFO] Running command: fastANI --query /var/lib/cwl/stg27b291b5-b015-4fb8-b074-85eca2a4ccff/GCF_003596335.1_ASM359633v1_genomic.fna.gz --refList GCF_003596335.1_ASM359633v1_genomic.fna/target_genomes.txt --output GCF_003596335.1_ASM359633v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:34,423] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:34,424] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf78ed2a0-4065-43c2-8680-4ec6b4336702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:34,425] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf78ed2a0-4065-43c2-8680-4ec6b4336702/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:34,447] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:19:34,447] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:19:34,447] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Motilimonas pumila	strain=PLHSC7-2	GCA_003596335.1	2303987	2303987	type	True	100.0	1436	1443	95	conclusive
Paraferrimonas haliotis	strain=AFRC7-2-1	GCA_002282895.1	2013866	2013866	type	True	83.523	61	1443	95	below_threshold
Motilimonas eburnea	strain=YH6	GCA_021295345.1	1737488	1737488	type	True	78.9078	241	1443	95	below_threshold
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	78.7584	265	1443	95	below_threshold
Vibrio comitans	strain=LMG 23416	GCA_024346835.1	413401	413401	type	True	77.9704	58	1443	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	77.9701	65	1443	95	below_threshold
Psychromonas ossibalaenae	strain=JAMM 0738	GCA_000381745.1	444922	444922	type	True	77.5629	61	1443	95	below_threshold
Agarivorans albus	strain=MKT 106	GCA_000414175.1	182262	182262	type	True	77.3306	91	1443	95	below_threshold
Agarivorans albus	strain=JCM 21469	GCA_019670105.1	182262	182262	type	True	77.2991	95	1443	95	below_threshold
Vibrio pectenicida	strain=LMG 19642	GCA_024347015.1	62763	62763	type	True	77.1428	51	1443	95	below_threshold
Aliagarivorans marinus	strain=DSM 23064	GCA_000429485.1	561965	561965	type	True	76.9772	60	1443	95	below_threshold
Photobacterium indicum	strain=ATCC 19614	GCA_003026215.1	81447	81447	type	True	76.9575	61	1443	95	below_threshold
Vibrio mimicus	strain=CAIM 602	GCA_000338875.1	674	674	type	True	76.9329	59	1443	95	below_threshold
Pseudoalteromonas spongiae	strain=UST010723-006	GCA_000238255.4	298657	298657	type	True	76.8738	53	1443	95	below_threshold
Vibrio mimicus	strain=NCTC11435	GCA_900460385.1	674	674	type	True	76.8693	60	1443	95	below_threshold
Photobacterium frigidiphilum	strain=JCM 12947	GCA_003025615.1	264736	264736	type	True	76.6179	62	1443	95	below_threshold
Shewanella avicenniae	strain=FJAT-51800	GCA_017354945.1	2814294	2814294	type	True	76.3311	52	1443	95	below_threshold
Pseudoalteromonas translucida	strain=KMM 520	GCA_001465295.1	166935	166935	type	True	76.2432	50	1443	95	below_threshold
Pseudoalteromonas fuliginea	strain=KMM 216	GCA_000690055.1	1872678	1872678	type	True	76.2049	50	1443	95	below_threshold
Pseudoalteromonas neustonica	strain=PAMC 28425	GCA_001653135.1	1840331	1840331	type	True	76.0768	58	1443	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:34,449] [INFO] DFAST Taxonomy check result was written to GCF_003596335.1_ASM359633v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:34,449] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:34,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:34,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf78ed2a0-4065-43c2-8680-4ec6b4336702/dqc_reference/checkm_data
[2024-01-24 15:19:34,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:34,500] [INFO] Task started: CheckM
[2024-01-24 15:19:34,500] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003596335.1_ASM359633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003596335.1_ASM359633v1_genomic.fna/checkm_input GCF_003596335.1_ASM359633v1_genomic.fna/checkm_result
[2024-01-24 15:20:10,819] [INFO] Task succeeded: CheckM
[2024-01-24 15:20:10,821] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:20:10,843] [INFO] ===== Completeness check finished =====
[2024-01-24 15:20:10,843] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:20:10,844] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003596335.1_ASM359633v1_genomic.fna/markers.fasta)
[2024-01-24 15:20:10,844] [INFO] Task started: Blastn
[2024-01-24 15:20:10,844] [INFO] Running command: blastn -query GCF_003596335.1_ASM359633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf78ed2a0-4065-43c2-8680-4ec6b4336702/dqc_reference/reference_markers_gtdb.fasta -out GCF_003596335.1_ASM359633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:20:12,011] [INFO] Task succeeded: Blastn
[2024-01-24 15:20:12,015] [INFO] Selected 29 target genomes.
[2024-01-24 15:20:12,015] [INFO] Target genome list was writen to GCF_003596335.1_ASM359633v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:20:12,038] [INFO] Task started: fastANI
[2024-01-24 15:20:12,038] [INFO] Running command: fastANI --query /var/lib/cwl/stg27b291b5-b015-4fb8-b074-85eca2a4ccff/GCF_003596335.1_ASM359633v1_genomic.fna.gz --refList GCF_003596335.1_ASM359633v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003596335.1_ASM359633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:33,338] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:33,353] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:20:33,353] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_003596335.1	s__Motilimonas pumila	100.0	1436	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Motilimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003318165.1	s__Psychromonas sp003318165	77.736	83	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104355.1	s__Photobacterium chitinilyticum	77.5657	52	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000381745.1	s__Psychromonas ossibalaenae	77.5629	61	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000414175.1	s__Agarivorans albus	77.3306	91	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	96.96	96.96	0.93	0.93	2	-
GCF_900537085.1	s__Agarivorans sp900537085	77.3139	91	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405585.1	s__Agarivorans sp005405585	77.2941	88	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Celerinatantimonadaceae;g__Agarivorans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026285.1	s__Photobacterium profundum	77.2103	58	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	99.97	99.97	1.00	1.00	2	-
GCF_004378355.1	s__Psychromonas sp004378355	77.1903	75	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013619145.1	s__Psychromonas sp013619145	77.0588	53	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003026215.1	s__Photobacterium indicum	76.9928	60	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176705.1	s__Pseudoalteromonas sp009176705	76.9499	54	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000338875.1	s__Vibrio mimicus	76.9329	59	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.40	96.81	0.94	0.91	26	-
GCF_004295665.1	s__Litorilituus sediminis	76.825	54	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Litorilituus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836415.1	s__Psychromonas sp002836415	76.7778	51	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003025615.1	s__Photobacterium frigidiphilum	76.6456	61	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	-
GCF_017354945.1	s__Shewanella sp017354945	76.3586	51	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000690055.1	s__Pseudoalteromonas fuliginea	76.2049	50	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	97.88	0.92	0.87	9	-
GCF_001653135.1	s__Pseudoalteromonas neustonica	76.097	57	1443	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	99.11	98.62	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 15:20:33,355] [INFO] GTDB search result was written to GCF_003596335.1_ASM359633v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:33,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:33,360] [INFO] DFAST_QC result json was written to GCF_003596335.1_ASM359633v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:33,360] [INFO] DFAST_QC completed!
[2024-01-24 15:20:33,360] [INFO] Total running time: 0h1m30s